interventions.diagnostics

interventions.diagnostics

Diagnostic products and delivery for TB testing.

Classes

Name	Description
CAD	CAD chest X-ray – simple, no age/HIV stratification.
Dx	TB diagnostic product defined by a DataFrame of state-to-result probabilities.
DxDelivery	Delivers a diagnostic product to eligible agents.
FujiLAM	FujiLAM – HIV-stratified, age-stratified.
OralSwab	Oral swab – age-stratified, TB-state-stratified.
Xpert	Xpert MTB/RIF – age-stratified (child/adult), TB-state-stratified.

CAD

interventions.diagnostics.CAD(df=None, datafile=None, **kwargs)

CAD chest X-ray – simple, no age/HIV stratification.

Dx

interventions.diagnostics.Dx(df, hierarchy=None, **kwargs)

TB diagnostic product defined by a DataFrame of state-to-result probabilities.

Parameters

Name	Type	Description	Default
df		DataFrame with required columns (state, result, probability) and optional filter columns (age_min, age_max, hiv). Only include filter columns relevant to the specific diagnostic.	required
hierarchy		List of result strings in priority order, e.g. [‘positive’, ‘negative’]. Agents in states not listed in df get the last entry (default negative).	None

DxDelivery

interventions.diagnostics.DxDelivery(
    product,
    coverage=1.0,
    eligibility=None,
    result_state='diagnosed',
    care_seeking_multiplier=1.0,
    result_validity=None,
    **kwargs,
)

Delivers a diagnostic product to eligible agents.

Handles eligibility (default: sought care, not yet diagnosed, alive), coverage filtering, result-state setting, and false-negative retry logic.

Parameters

Name	Type	Description	Default
product		A Dx product instance.	required
coverage		Fraction of eligible agents tested (float or ss.Dist). Default 1.0.	1.0
eligibility		Callable (sim) -> uids. Default: sought_care & ~diagnosed & alive.	None
result_state		People-state name set True on positive result. Default ‘diagnosed’.	'diagnosed'
care_seeking_multiplier		Multiplier on care-seeking rate for false negatives. Default 1.0.	1.0

Methods

Name	Description
shrink	Delete temporary results
step	Main step method: see submethods for details.
step_administer	Administer diagnostic product to selected UIDs and return results.
step_expire_results	Reset result states that have exceeded the validity window
step_select_eligible	Return eligible UIDs for this step.
step_update_states	Update states associated with diagnostic results
update_results	Store results

shrink

interventions.diagnostics.DxDelivery.shrink()

Delete temporary results

step

interventions.diagnostics.DxDelivery.step()

Main step method: see submethods for details.

step_administer

interventions.diagnostics.DxDelivery.step_administer()

Administer diagnostic product to selected UIDs and return results.

step_expire_results

interventions.diagnostics.DxDelivery.step_expire_results()

Reset result states that have exceeded the validity window

step_select_eligible

interventions.diagnostics.DxDelivery.step_select_eligible()

Return eligible UIDs for this step.

step_update_states

interventions.diagnostics.DxDelivery.step_update_states()

Update states associated with diagnostic results

update_results

interventions.diagnostics.DxDelivery.update_results()

Store results

FujiLAM

interventions.diagnostics.FujiLAM(df=None, datafile=None, **kwargs)

FujiLAM – HIV-stratified, age-stratified.

OralSwab

interventions.diagnostics.OralSwab(df=None, datafile=None, **kwargs)

Oral swab – age-stratified, TB-state-stratified.

Xpert

interventions.diagnostics.Xpert(df=None, datafile=None, **kwargs)

Xpert MTB/RIF – age-stratified (child/adult), TB-state-stratified.